PXD017081 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Large-scale discovery of non-canonical peptides in monocot and dicot plants through an integrated peptidogenomic pipelineLarge-scale discovery of non-canonical peptides in monocot and dicot plants through an integrated peptidogenomic pipeline |
Description | Non-canonical peptides (NCPs) have been shown to play critical roles in fundamental biological processes. Despite their importance, NCPs have been rarely identified and characterized in plants. Here we developed an integrated peptidogenomic pipeline using high-throughput mass spectra to probe customized six-frame translation database and for the first time applied this pipeline to large-scale identification of NCPs in both monocot and dicot plants. Altogether, 1,993 and 1,860 NCPs were unambiguously identified in maize and Arabidopsis, respectively. The NCPs showed distinct characteristics compared to canonical peptides and can be derived from introns, 3’UTRs, 5’UTRs, junctions and intergenic regions. These results revealed that non-canonical translation or cryptic translation events occur more universally than previously thought. In addition, maize NCPs were found enriched within the regions associated with phenotypic variation or regions under domestication selection, indicating their potential function in plant genetic regulations of complex traits and evolution. Summarily, this study provides the first unbiased and global view of plant NCPs. The identification of large-scale NCPs in both monocot and dicot plants reveals that a much larger portion of the plant genome can be translated biologically functional molecules, which has important implications in functional genomic studies. The present study also provides a useful resource for the characterization of more hidden NCPs in other plants. |
HostingRepository | PRIDE |
AnnounceDate | 2020-08-11 |
AnnouncementXML | Submission_2020-08-10_23:57:47.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Shunxi Wang |
SpeciesList | scientific name: Zea mays (Maize); NCBI TaxID: 4577; |
ModificationList | No PTMs are included in the dataset |
Instrument | Q Exactive |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2020-01-13 07:23:03 | ID requested | |
⏵ 1 | 2020-08-10 23:57:47 | announced | |
Publication List
Wang S, Tian L, Liu H, Li X, Zhang J, Chen X, Jia X, Zheng X, Wu S, Chen Y, Yan J, Wu L, Large-Scale Discovery of Non-conventional Peptides in Maize and Arabidopsis through an Integrated Peptidogenomic Pipeline. Mol Plant, 13(7):1078-1093(2020) [pubmed] |
Keyword List
submitter keyword: Non-canonical peptides, Peptidogenomics, Mass spectrometry, Six-frame translation, Plants |
Contact List
Liuji Wu |
contact affiliation | Henan agricultural university |
contact email | wlj200120@163.com |
lab head | |
Shunxi Wang |
contact affiliation | Henan agricultural university |
contact email | wangshunxi2008@163.com |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
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[ - ]
- PRIDE
- PXD017081
- Label: PRIDE project
- Name: Large-scale discovery of non-canonical peptides in monocot and dicot plants through an integrated peptidogenomic pipelineLarge-scale discovery of non-canonical peptides in monocot and dicot plants through an integrated peptidogenomic pipeline